bims-librar Biomed News on Biomedical librarianship
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Issue of 2021‒04‒11 │
twelve papers selected by │
Thomas Krichel (Open Library │
Society) │
http://e.biomed.news/librar │
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1. Learning about COVID-19: a qualitative interview study of Australians'
use of information sources.
2. REDASA: A Secure Continually Updating Web-Source Processing Pipeline
supporting a REaltime DAta Synthesis and Analysis of Scientific
Literature.
3. A Novel Web Application for Rapidly Searching the Diagnostic Case
Archive.
4. A Comparative Analysis of System Features Used in the TREC-COVID
Information Retrieval Challenge.
5. Search, access, and explore life science nanopublications on the Web.
6. TransforMED: End-to-End Transformers for Evidence-Based Medicine and
Argument Mining in medical literature.
7. Citation.js: a format-independent, modular bibliography tool for the
browser and command line.
8. Influence of tweets and diversification on serendipitous research
paper recommender systems.
9. Which Resources Are Better: Sales or Scholarly? An Assessment on the
Readability, Quality, and Technical Features of Online Chemical Peel
Websites.
10. The readability of general practice websites: a cross-sectional
analysis of all general practice websites in Scotland.
11. A READABILITY COMPARISON OF ONLINE SPANISH AND ENGLISH PATIENT
EDUCATION MATERIALS ABOUT VISION HEALTH.
12. Predatory Journals, Fake Conferences and Misleading Social Media: The
Dark Side of Medical Information.
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BMC Public Health. 2021 Apr 07. 21(1): 662
1. Learning about COVID-19: a qualitative interview study of Australians'
use of information sources.
Lupton D, Lewis S
BACKGROUND: A multitude of information sources are available to publics when
novel infectious diseases first emerge. In this paper, we adopt a
qualitative approach to investigate how Australians learnt about the novel
coronavirus and COVID-19 and what sources of information they had found most
useful and valuable during the early months of the pandemic.
METHODS: In-depth semi-structured telephone interviews were conducted with a
diverse group of 40 Australian adults in mid-2020 about their experiences of
the COVID-19 crisis. Participants were recruited through Facebook
advertising. Detailed case studies were created for each participant,
providing the basis of a thematic analysis which focused on the
participants' responses to the questions about COVID-19-related information
sources.
RESULTS: Diverse sources of COVID-19-related information, including
traditional media, online media and in-person interactions, were actively
accessed, appraised and engaged with by participants. There was a high level
of interest in COVID-19 information as people grappled with uncertainty,
anxiety and feeling overwhelmed. Certain key events or experiences made
people become aware that the outbreak was threatening Australia and
potentially themselves. Most people demonstrated keen awareness that
misinformation was rife in news outlets and social media sites and that they
were taking steps to determine the accuracy of information. High trust was
placed in health experts, scientists and government sources to provide
reliable information. Also important to participants were informal
discussions with friends and family members who were experts or working in
relevant fields, as well as engaging in-person in interactions and hearing
from friends and family who lived overseas about what COVID-19 conditions
were like there.
CONCLUSION: A constantly changing news environment raises challenges for
effective communication of risk and containment advice. People can become
confused, distressed and overwhelmed by the plethora of information sources
and fast-changing news environment. On the other hand, seeking out
information can provide reassurance and comfort in response to anxiety and
uncertainty. Clarity and consistency in risk messaging is important, as is
responding quickly to changes in information and misinformation. Further
research should seek to identify any changes in use of and trust in
information sources as time goes by.
DOI: https://doi.org/10.1186/s12889-021-10743-7
URL: http://pubmed.ncbi.nlm.nih.gov/33823843
J Med Internet Res. 2021 Apr 03.
2. REDASA: A Secure Continually Updating Web-Source Processing Pipeline
supporting a REaltime DAta Synthesis and Analysis of Scientific
Literature.
Vaghela U, Rabinowicz S, Bratsos P, Martin G, Fritzilas E, Markar S,
Purkayastha S, Stringer K, Singh H, Llewellyn C, Dutta D, Clarke JM, Howard
M, Serban O, Kinross J
BACKGROUND: The scale and quality of the global scientific response to the
COVID-19 pandemic has unquestionably saved lives. However, COVID-19 has also
triggered an unprecedented "infodemic"; the velocity and volume of data
production has overwhelmed many key stakeholders such as clinicians and
policymakers who have been unable to process structured and unstructured
data for evidence-based decision making. Current solutions which aim to
alleviate this data synthesis challenge are unable to capture heterogeneous
web data in "real-time" for the production of concomitant answers and are
not based on the high-quality information in response to a free-text query.
OBJECTIVE: : The main objective of this project is to build a generic
real-time continuously updating curation platform that could support a data
synthesis and analysis of scientific literature framework. Our secondary
objective is to validate this pipeline and the curation methodology on
COVID-19 related medical literature, by expanding the CORD19 dataset by
adding new, unstructured data.
METHODS: To realise an infrastructure that addresses the objectives, the
PanSurg Collaborative at Imperial College London has developed a unique data
pipeline based on a web crawler extraction methodology. This data pipeline
converges with a novel curation methodology that adopts a "human in the
loop" methodology for the characterisation of quality, relevance and key
evidence across a range of scientific literature sources.
RESULTS: REDASA is now one of the world's largest and most current COVID-19
source of evidence consisting of 104,000 documents. By capturing curators'
critical appraisal methodology through the application of discrete labelling
and rating of information, REDASA has rapidly developed a foundational data
science dataset of over 1400 articles in the realm of pooled COVID-19
information, representing ∼10% of the papers written worldwide on COVID-19
in under two weeks.
CONCLUSIONS: This dataset can act as ground-truth for future implementation
of a live, automated systematic review. The benefits of the current design
are threefold: 1) adoption of a friendlier "human in the loop" methodology
by embedding an efficient user-friendly curation platform into an NLP search
engine; 2) provides a curated dataset in JSON (JavaScript Object Notation)
format for experienced academic reviewers' critical appraisal choices and
decision-making methodology; 3) due to the wide scope and depth of the
web-crawling, REDASA has already captured one of the world's largest
COVID-19 data corpora for search and curation. This dataset can act as
ground-truth for future implementation of a live, automated systematic
review.
DOI: https://doi.org/10.2196/25714
URL: http://pubmed.ncbi.nlm.nih.gov/33835932
J Pathol Inform. 2020 ;11 39
3. A Novel Web Application for Rapidly Searching the Diagnostic Case
Archive.
Robertson S
Academic pathologists must have the ability to search their institution's
archive of diagnostic case data. This ability is foundational for research,
education, and other academic activities. However, the built-in search
functions of commercial laboratory information systems are not always
optimized for this activity, leading to delays between an initial search
request, and eventual results delivery. To solve this problem, a novel
web-based search platform was developed, named Pathtools, which allows our
staff and trainees to directly and rapidly search our diagnostic case
archive. Pathtools was built with open-source components and features a
web-based user-interface. Pathtools uses an SQL database which was populated
with anatomic pathology case data going back to 1980, and contains 4.2
million cases (as of July 31, 2020). Pathtools has two major modes of
operation, "Preview Mode" and "Research Mode." Since deployment in February
of 2019, Pathtools carried out 33,817 searches in Preview Mode, averaging
0.72 s (standard deviation = 1.7) between search submission, and on-screen
display of search results. In Research Mode, Pathtools has also been used to
produce data sets for research activity, providing the data used in many
abstracts and manuscripts our investigators submitted recently.
Interestingly, 75% of search activity is from trainees during their preview
time. In a survey of residents and fellows, 83% used Pathtools during the
majority of their preview sessions, demonstrating an important role for this
resource in trainee education. In conclusion, a web-based search tool can
rapidly and securely provide search capability directly to end-users, which
has augmented trainee education and research activity in our department.
Keywords: Education; pathology reports; python; text search; web
application
DOI: https://doi.org/10.4103/jpi.jpi_43_20
URL: http://pubmed.ncbi.nlm.nih.gov/33828897
J Biomed Inform. 2021 Apr 05. pii: S1532-0464(21)00074-5.
4. A Comparative Analysis of System Features Used in the TREC-COVID
Information Retrieval Challenge.
Chen J, Hersh WR
The COVID-19 pandemic has resulted in a rapidly growing quantity of
scientific publications from journal articles, preprints, and other sources.
The TREC-COVID Challenge was created to evaluate information retrieval
methods and systems for this quickly expanding corpus. Using the COVID-19
Open Research Dataset (CORD-19), several dozen research teams participated
in over 5 rounds of the TREC-COVID Challenge. While previous work has
compared IR techniques used on other test collections, there are no studies
that have analyzed the methods used by participants in the TREC-COVID
Challenge. We manually reviewed team run reports from Rounds 2 and 5,
extracted features from the documented methodologies, and used a univariate
and multivariate regression-based analysis to identify features associated
with higher retrieval performance. We observed that fine-tuning datasets
with relevance judgments, MS-MARCO, and CORD-19 document vectors was
associated with improved performance in Round 2 but not in Round 5. Though
the relatively decreased heterogeneity of runs in Round 5 may explain the
lack of significance in that round, fine-tuning has been found to improve
search performance in previous challenge evaluations by improving a system's
ability to map relevant queries and phrases to documents. Furthermore, term
expansion was associated with improvement in system performance, and the use
of the narrative field in the TREC-COVID topics was associated with
decreased system performance in both rounds. These findings emphasize the
need for clear queries in search. While our study has some limitations in
its generalizability and scope of techniques analyzed, we identified some IR
techniques that may be useful in building search systems for COVID-19 using
the TREC-COVID test collections.
DOI: https://doi.org/10.1016/j.jbi.2021.103745
URL: http://pubmed.ncbi.nlm.nih.gov/33831536
PeerJ Comput Sci. 2021 ;7 e335
5. Search, access, and explore life science nanopublications on the Web.
Giachelle F, Dosso D, Silvello G
Nanopublications are Resource Description Framework (RDF) graphs encoding
scientific facts extracted from the literature and enriched with provenance
and attribution information. There are millions of nanopublications
currently available on the Web, especially in the life science domain.
Nanopublications are thought to facilitate the discovery, exploration, and
re-use of scientific facts. Nevertheless, they are still not widely used by
scientists outside specific circles; they are hard to find and rarely cited.
We believe this is due to the lack of services to seek, find and understand
nanopublications' content. To this end, we present the NanoWeb application
to seamlessly search, access, explore, and re-use the nanopublications
publicly available on the Web. For the time being, NanoWeb focuses on the
life science domain where the vastest amount of nanopublications are
available. It is a unified access point to the world of nanopublications
enabling search over graph data, direct connections to evidence papers, and
scientific curated databases, and visual and intuitive exploration of the
relation network created by the encoded scientific facts.
Keywords: Data access; Data citation; Data exploration; Data search; Graph
exploration; Nanopublication; Scientific data
DOI: https://doi.org/10.7717/peerj-cs.335
URL: http://pubmed.ncbi.nlm.nih.gov/33816986
J Biomed Inform. 2021 Mar 31. pii: S1532-0464(21)00096-4.
6. TransforMED: End-to-End Transformers for Evidence-Based Medicine and
Argument Mining in medical literature.
Stylianou N, Vlahavas I
Argument Mining (AM) refers to the task of automatically identifying
arguments in a text and finding their relations. In medical literature this
is done by identifying Claims and Premises and classifying their relations
as either Support or Attack. Evidence-Based Medicine (EBM) refers to the
task of identifying all related evidence in medical literature to allow
medical practitioners to make informed choices and form accurate treatment
plans. This is achieved through the automatic identification of Population,
Intervention, Comparator and Outcome entities (PICO) in the literature to
limit the collection to only the most relevant documents. In this work, we
combine EBM with AM in medical literature to increase the performance of the
individual models and create high quality argument graphs, annotated with
PICO entities. To that end, we introduce a state-of-the-art EBM model, used
to predict the PICO entities and two novel Argument Identification and
Argument Relation classification models that utilize the PICO entities to
enhance their performance. Our final system works in a pipeline and is able
to identify all PICO entities in a medical publication, the arguments
presented in them and their relations.
Keywords: Argument Mining; Deep Learning; Evidence Based Medicine; Natural
Language Processing
DOI: https://doi.org/10.1016/j.jbi.2021.103767
URL: http://pubmed.ncbi.nlm.nih.gov/33811985
PeerJ Comput Sci. 2019 ;5 e214
7. Citation.js: a format-independent, modular bibliography tool for the
browser and command line.
Willighagen LG
Background: Given the vast number of standards and formats for
bibliographical data, any program working with bibliographies and citations
has to be able to interpret such data. This paper describes the development
of Citation.js (https://citation.js.org/), a tool to parse and format
according to those standards. The program follows modern guidelines for
software in general and JavaScript in specific, such as version control,
source code analysis, integration testing and semantic versioning.
Results: The result is an extensible tool that has already seen adaption in
a variety of sources and use cases: as part of a server-side page generator
of a publishing platform, as part of a local extensible document generator,
and as part of an in-browser converter of extracted references. Use cases
range from transforming a list of DOIs or Wikidata identifiers into a BibTeX
file on the command line, to displaying RIS references on a webpage with
added Altmetric badges to generating "How to cite this" sections on a blog.
The accuracy of conversions is currently 27% for properties and 60% for
types on average and a typical initialization takes 120 ms in browsers and 1
s with Node.js on the command line.
Conclusions: Citation.js is a library supporting various formats of
bibliographic information in a broad selection of use cases and
environments. Given the support for plugins, more formats can be added with
relative ease.
Keywords: Bibliography; Javascript
DOI: https://doi.org/10.7717/peerj-cs.214
URL: http://pubmed.ncbi.nlm.nih.gov/33816867
PeerJ Comput Sci. 2020 ;6 e273
8. Influence of tweets and diversification on serendipitous research
paper recommender systems.
Nishioka C, Hauke J, Scherp A
In recent years, a large body of literature has accumulated around the topic
of research paper recommender systems. However, since most studies have
focused on the variable of accuracy, they have overlooked the serendipity of
recommendations, which is an important determinant of user satisfaction.
Serendipity is concerned with the relevance and unexpectedness of
recommendations, and so serendipitous items are considered those which
positively surprise users. The purpose of this article was to examine two
key research questions: firstly, whether a user's Tweets can assist in
generating more serendipitous recommendations; and secondly, whether the
diversification of a list of recommended items further improves serendipity.
To investigate these issues, an online experiment was conducted in the
domain of computer science with 22 subjects. As an evaluation metric, we use
the serendipity score (SRDP), in which the unexpectedness of recommendations
is inferred by using a primitive recommendation strategy. The results
indicate that a user's Tweets do not improve serendipity, but they can
reflect recent research interests and are typically heterogeneous.
Contrastingly, diversification was found to lead to a greater number of
serendipitous research paper recommendations.
Keywords: Digital library; Experimental study; Recommender system;
Scholarly articles; Serendipity; User study
DOI: https://doi.org/10.7717/peerj-cs.273
URL: http://pubmed.ncbi.nlm.nih.gov/33816924
Aesthet Surg J Open Forum. 2021 Jan;3(1): ojab008
9. Which Resources Are Better: Sales or Scholarly? An Assessment on the
Readability, Quality, and Technical Features of Online Chemical Peel
Websites.
Varghese JA, Patel AA, Joshi C, Alleyne B, Galiano RD
Background: Chemical peels are an exceedingly popular cosmetic treatment
with a wide variety of suppliers, each with its own online health resource
describing the procedure. With increasing reliance on the internet for
medical information, it is crucial that these resources provide reliable
information for patients to make informed decisions.
Objectives: The aim of this study was to examine popular chemical peel
resources and determine if those that offered chemical peel treatments
(Sales) had lower readability, quality of information, and technical
features compared with those that did not (Scholarly).
Methods: The term "chemical peel" was searched in July 2020 and the top 50
websites were retrieved for analysis. Each resource's readability, quality,
and technical features were measured through 8 readability formulas, the
DISCERN and Health on the Net Code (HONcode), and 2 website performance
monitors.
Results: The 50 websites were analyzed with an average Fry readability score
of 13th grade. Scholarly websites displayed higher readability than Sales
(Flesch Reading Ease 54.4 > 47.4, P = 0.047 and Coleman-Liau Index 10.6 <
11.7, P = 0.04). Scholarly resources surpassed Sales both in quality
(DISCERN 56.4 > 39.7, P < 0.001 and HONcode 11.8 > 9.5, P = 0.032) and
technical features (WooRank 76.9 > 68.6, P = 0.0082).
Conclusions: The average readability of chemical peel resources is too
difficult, and their quality must be improved. Scholarly resources exhibited
higher readability, quality, and technical features than Sales websites.
DOI: https://doi.org/10.1093/asjof/ojab008
URL: http://pubmed.ncbi.nlm.nih.gov/33824950
Br J Gen Pract. 2021 Jan 05. pii: BJGP.2020.0820. [Epub ahead of print]
10. The readability of general practice websites: a cross-sectional
analysis of all general practice websites in Scotland.
Rughani G, Hanlon P, Corcoran N, Mair FS
BACKGROUND: General practice websites are an increasingly important point of
interaction, but their readability is largely unexplored. One in four adults
struggle with basic literacy, and there is a socioeconomic gradient.
Readable content is a prerequisite to promoting health literacy.
AIM: To assess general practice website readability by analysing text and
design factors, and to assess whether practices adapted their website text
to the likely literacy levels of their populations.
DESIGN AND SETTING: Websites for all general practices across Scotland were
analysed from March to December 2019, using a cross-sectional design.
METHOD: Text was extracted from five webpages per website and eight text
readability factors were measured, including the Flesch Reading Ease and the
Flesch-Kincaid Grade Level. The relationship between readability and a
practice population's level of deprivation, measured using the Scottish
Index of Multiple Deprivation (SIMD), was assessed. Overall, 10 design
factors contributing to readability and accessibility were scored.
RESULTS: In total, 86.4% (n = 813/941) of Scottish practices had a website;
22.9% (n = 874/3823) of webpages were written at, or below, the
government-recommended reading level for online content (9-14 years old),
and the content of the remaining websites, 77.1% (n = 2949/3823), was
suitable for a higher reading age. Of all webpages, 80.5% (n = 3077/3823)
were above the recommended level for easy-to-understand 'plain English'.
There was no statistically significant association between webpage reading
age and SIMD. Only 6.7% (n = 51/764) of websites achieved all design and
accessibility recommendations.
CONCLUSION: Changes to practice websites could improve readability and
promote health literacy, but practices will need financial resources and
ongoing technical support if this is to be achieved and maintained. Failure
to provide readable and accessible websites may widen health inequalities;
the topic will become increasingly important as online service use
accelerates.
Keywords: digital divide; general practice; health literacy; online
systems; primary health care
DOI: https://doi.org/10.3399/BJGP.2020.0820
URL: http://pubmed.ncbi.nlm.nih.gov/33824159
Ophthalmic Epidemiol. 2021 Apr 08. 1-7
11. A READABILITY COMPARISON OF ONLINE SPANISH AND ENGLISH PATIENT
EDUCATION MATERIALS ABOUT VISION HEALTH.
Karthik N, Barekatain K, Vu H, Wu DTY, Ehrlich JR
Purpose: Current United States national guidelines recommend patient
education materials (PEMs) be written at a 5th-6th grade level. The
objective of this study was to compare the readability of Spanish vision and
eye health PEMs to nationally recommended reading levels and to English
versions of the same PEMs.Methods: PEMs were collected from seven online
websites of vision-related organizations that provided PEMs with Spanish and
English versions. PEMs were downloaded for text to be extracted and
analyzed. Readability scoring was performed with Índice Flesch-Szigriszt,
Spanish and English Lexile Text Analyzers, and Flesch-Kincaid Grade
Level.Results: A total of 484 PEMs with Spanish and English versions were
analyzed. Readability for Spanish PEMs was reported at or above the 6th
grade level for 57% of articles based on Spanish Lexile scoring and 63%
based on Índice Flesch-Szigriszt scoring. Readability for English PEMs
was reported at or above the 6th grade level for 66% of articles based on
English Lexile scoring and 75% based on Flesch-Kincaid Grade Level scoring.
Wilcoxon signed-rank test comparing grade levels translated from Lexile
scores for Spanish and English versions of PEMs revealed that Spanish
versions of PEMs required higher grade reading levels compared to English
versions of PEMs (p < .001).Conclusion: Spanish and English PEMs were
written above nationally recommended reading levels. Online sources
providing multilingual vision and eye health education should consider
routinely monitoring PEMs to ensure reading levels meet the literacy needs
of their audiences.
Keywords: Readability; health literacy; internet; patient education;
vision and eye health
DOI: https://doi.org/10.1080/09286586.2021.1910316
URL: http://pubmed.ncbi.nlm.nih.gov/33832394
Zdr Varst. 2021 Jun;60(2): 79-81
12. Predatory Journals, Fake Conferences and Misleading Social Media: The
Dark Side of Medical Information.
Kert S, Švab I
We live in an age of information revolution, where trends in informing
physicians and the lay public bring new challenges that must be faced by
healthcare professionals. Predatory journals and fake conferences are
common. Social media is full of false information, which results in serious
public health damage. Therefore, it is important that health professionals
communicate properly with the public and patients and that they address the
education of both the public and other health professionals.
Keywords: evidence-based medicine; fake medicine; infodemic;
misinformation; predatory journals
DOI: https://doi.org/10.2478/sjph-2021-0012
URL: http://pubmed.ncbi.nlm.nih.gov/33822833
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